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Access to General Feature Format databases created with Bio::DB:GFF
based on documentation for Lincoln Stein's Perl Bio::DB::GFF
>>> import os >>> import Bio.GFF >>> PASSWORD = os.environ['MYSQLPASS'] >>> DATABASE_GFF = 'wormbase_ws93' >>> FASTADIR = '/local/wormbase_ws93/' >>> gff = Bio.GFF.Connection(passwd=PASSWORD, db=DATABASE_GFF, fastadir=FASTADIR)
Version: $Revision: 1.8 $
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Segment this will only work for the simplest of easy.Location objects |
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Connection Connection to GFF database |
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RetrieveSeqname Singleton: contain records of loaded FASTA files |
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Feature strand may be: +/0 = Watson -/1 = Crick |
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FeatureQueryRow row of FeatureQuery results works like a Feature |
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FeatureQuery SELECT fdata.fref AS seqname,... |
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FeatureAggregate |
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DEFAULT_ALPHABET = IUPACUnambiguousDNA()
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standard_translator = Translate.unambiguous_dna_by_id [1]
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